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Boettger JD, Neubauer C, Kopf SH, Kubicki JD. Microbial Denitrification: Active Site and Reaction Path Models Predict New Isotopic Fingerprints. ACS EARTH & SPACE CHEMISTRY 2022; 6:2582-2594. [PMID: 36425342 PMCID: PMC9677970 DOI: 10.1021/acsearthspacechem.2c00102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 08/28/2022] [Accepted: 09/02/2022] [Indexed: 06/16/2023]
Abstract
The study of isotopic fingerprints in nitrate (δ15N, δ18O, Δ17O) has enabled pivotal insights into the global nitrogen cycle and revealed new knowledge gaps. Measuring populations of isotopic homologs of intact NO3 - ions (isotopologues) shows promise to advance the understanding of nitrogen cycling processes; however, we need new theory and predictions to guide laboratory experiments and field studies. We investigated the hypothesis that the isotopic composition of the residual nitrate pool is controlled by the N-O bond-breaking step in Nar dissimilatory nitrate reductase using molecular models of the enzyme active sites and associated kinetic isotope effects (KIEs). We integrated the molecular model results into reaction path models representing the reduction of nitrate under either closed-system or steady-state conditions. The predicted intrinsic KIE (15ε and 18ε) of the Nar active site matches observed fractionations in both culture and environmental studies. This is what would be expected if the isotopic composition of marine nitrate were controlled by dissimilatory nitrate reduction by Nar. For a closed system, the molecular models predict a pronounced negative 15N-18O clumping anomaly in residual nitrate. This signal could encode information about the amount of nitrate consumed in a closed system and thus constrain initial nitrate concentration and its isotopic composition. Similar clumped isotope anomalies can potentially be used to distinguish whether a system is open or closed to new nitrate addition. These mechanistic predictions can be tested and refined in combination with emerging ESI-Orbitrap measurements.
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Affiliation(s)
- Jason D. Boettger
- Department
of Earth, Environmental, and Resource Sciences, The University of Texas at El Paso, El Paso, Texas 79968, United States
| | - Cajetan Neubauer
- Department
of Geological Sciences & Institute of Arctic and Alpine Research, University of Colorado, Boulder, Colorado 80303, United States
| | - Sebastian H. Kopf
- Department
of Geological Sciences & Institute of Arctic and Alpine Research, University of Colorado, Boulder, Colorado 80303, United States
| | - James D. Kubicki
- Department
of Earth, Environmental, and Resource Sciences, The University of Texas at El Paso, El Paso, Texas 79968, United States
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2
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Enzymatic N N bond formation: Mechanism for the N-nitroso synthesis catalyzed by non-heme iron SznF enzyme. J Catal 2021. [DOI: 10.1016/j.jcat.2021.04.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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3
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Yu MJ, Wu J, Chen SL. Mechanism and Inhibitor Exploration with Binuclear Mg Ketol-Acid Reductoisomerase: Targeting the Biosynthetic Pathway of Branched-Chain Amino Acids. Chembiochem 2019; 21:381-391. [PMID: 31309701 DOI: 10.1002/cbic.201900363] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2019] [Indexed: 01/01/2023]
Abstract
Binuclear Mg ketol-acid reductoisomerase (KARI), which converts (S)-2-acetolactate into (R)-2,3-dihydroxyisovalerate, is responsible for the second step of the biosynthesis of branched-chain amino acids in plants and microorganisms and thus serves as a key inhibition target potentially without effects on mammals. Here, through the use of density functional calculations and a chemical model, the KARI-catalyzed reaction has been demonstrated to include the initial deprotonation of the substrate C2 hydroxy group, bridged by the two Mg ions, alkyl migration from the C2-alkoxide carbon atom to the C3-carbonyl carbon atom, and hydride transfer from a nicotinamide adenine dinucleotide phosphate [NAD(P)H] cofactor to C2. A dead-end mechanism with a hydride transferred to the C3 carbonyl group has been ruled out. The nucleophilicity (migratory aptitude) of the migrating carbon atom and the provision of additional negative charge to the di-Mg coordination sphere have significant effects on the steps of alkyl migration and hydride transfer, respectively. Other important mechanistic characteristics are also revealed. Inspired by the mechanism, an inhibitor (2-carboxylate-lactic acid) was designed and predicted by barrier analysis to be effective in inactivating KARI, hence probably enriching the antifungal and antibacterial library. Two types of slow substrate analogues (2-trihalomethyl acetolactic acids and 2-glutaryl lactic acid) were also found.
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Affiliation(s)
- Ming-Jia Yu
- Key Laboratory of Cluster Science of the Ministry of Education, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 100081, P. R. China
| | - Jue Wu
- Key Laboratory of Cluster Science of the Ministry of Education, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 100081, P. R. China
| | - Shi-Lu Chen
- Key Laboratory of Cluster Science of the Ministry of Education, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 100081, P. R. China
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4
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Teixeira CSS, Ramos MJ, Sousa SF, Cerqueira NMFSA. Solving the Catalytic Mechanism of Tryptophan Synthase: an Emergent Drug Target in the Treatment of Tuberculosis. ChemCatChem 2019. [DOI: 10.1002/cctc.201901505] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Carla S. Silva Teixeira
- UCIBIO@REQUIMTEBioSIMDepartamento de BiomedicinaFaculdade de MedicinaUniversidade do Porto Porto 4200-319 Portugal
| | - Maria J. Ramos
- UCIBIO@REQUIMTEDepartamento de Química e BioquímicaFaculdade de CiênciasUniversidade do Porto Porto 4169-007 Portugal
| | - Sérgio F. Sousa
- UCIBIO@REQUIMTEBioSIMDepartamento de BiomedicinaFaculdade de MedicinaUniversidade do Porto Porto 4200-319 Portugal
| | - Nuno M. F. S. A. Cerqueira
- UCIBIO@REQUIMTEBioSIMDepartamento de BiomedicinaFaculdade de MedicinaUniversidade do Porto Porto 4200-319 Portugal
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5
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Sun SQ, Chen SL. How does Mo-dependent perchlorate reductase work in the decomposition of oxyanions? Dalton Trans 2019; 48:5683-5691. [DOI: 10.1039/c9dt00863b] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The mechanisms of Mo-dependent perchlorate reductase (PcrAB)-catalyzed decomposition of perchlorate, bromate, iodate, and nitrate were revealed by density functional calculations.
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Affiliation(s)
- Shuo-Qi Sun
- Key Laboratory of Cluster Science of Ministry of Education
- School of Chemistry and Chemical Engineering
- Beijing Institute of Technology
- Beijing 100081
- China
| | - Shi-Lu Chen
- Key Laboratory of Cluster Science of Ministry of Education
- School of Chemistry and Chemical Engineering
- Beijing Institute of Technology
- Beijing 100081
- China
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6
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Fortino M, Marino T, Russo N, Sicilia E. Mechanistic investigation of trimethylamine-N-oxide reduction catalysed by biomimetic molybdenum enzyme models. Phys Chem Chem Phys 2017; 18:8428-36. [PMID: 26932500 DOI: 10.1039/c5cp07278f] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this paper, we report a theoretical investigation of the reduction reaction mechanism of Me3NO using molybdenum containing systems that are functional and structural analogues of trimethylamine N-oxide reductase mononuclear molybdenum enzyme. The reactivity of the monooxomolybdenum(IV) benzenedithiolato complex and its derivatives to carbamoyl (t-BuNHCO) and acylamino (t-BuCONH) substituents on the benzene rings in both cis and trans arrangements was explored. The calculated energy profiles describing the steps of two mechanisms of attack considered viable (named cis- and trans-attack) by the Me3NO substrate at cis and trans positions with respect to the oxo ligand show that the attack on cis is energetically more favourable than the attack on trans. Along the pathway for the cis-attack the first step of the reaction, that is rate-determining for all the studied compounds, is the approach of the substrate to the Mo centre in cis to the oxo ligand that causes a distortion of the initial square-pyramidal geometry of the complex. The reaction steps involved in the trans position attack were also explored. Calculations confirm that, as previously suggested, the introduction of ligands able to form intramolecular NH···S hydrogen bonds accelerates the reduction of the Me3NO substrate and contributes to the tuning of the reactivity of molybdoenzyme models.
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Affiliation(s)
- M Fortino
- Department of Chemistry and Chemical Technologies, Università della Calabria, 87036, Arcavacata di Rende, Italy.
| | - T Marino
- Department of Chemistry and Chemical Technologies, Università della Calabria, 87036, Arcavacata di Rende, Italy.
| | - N Russo
- Department of Chemistry and Chemical Technologies, Università della Calabria, 87036, Arcavacata di Rende, Italy.
| | - E Sicilia
- Department of Chemistry and Chemical Technologies, Università della Calabria, 87036, Arcavacata di Rende, Italy.
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7
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Lan CL, Chen SL. The Decarboxylation of α,β-Unsaturated Acid Catalyzed by Prenylated FMN-Dependent Ferulic Acid Decarboxylase and the Enzyme Inhibition. J Org Chem 2016; 81:9289-9295. [PMID: 27618344 DOI: 10.1021/acs.joc.6b01872] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ferulic acid decarboxylase (Fdc1) is able to catalyze the decarboxylation of α,β-unsaturated acids using a novel cofactor, prenylated flavin mononucleotide (PrFMN). Using density functional theory calculations, we here have investigated the Fdc1 reaction mechanism with the substrate of α-methylcinnamic acid. It is demonstrated that Fdc1 employs a 1,3-dipolar cycloaddition mechanism involving four concerted steps, where the Glu282 acts as a crucial proton donor to protonate the α carbon (Cα). The last step, the decomposition of a pyrrolidine species, is rate-limiting with an overall barrier of 18.9 kcal mol-1. Furthermore, when α-hydroxycinnamic acid is used, the Glu282 is found to have another face to transport the hydroxyl proton to the Cβ atom to promote the tautomerization from enol intermediate to ketone species leading to the inhibition of the Fdc1 enzyme. The PrFMN roles are also discussed in detail.
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Affiliation(s)
- Cui-Lan Lan
- Key Laboratory of Cluster Science of Ministry of Education, School of Chemistry and Chemical Engineering, Beijing Institute of Technology , Beijing 100081, China
| | - Shi-Lu Chen
- Key Laboratory of Cluster Science of Ministry of Education, School of Chemistry and Chemical Engineering, Beijing Institute of Technology , Beijing 100081, China
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8
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Dułak M, Kamiński JW, Wesołowski TA. Equilibrium Geometries of Noncovalently Bound Intermolecular Complexes Derived from Subsystem Formulation of Density Functional Theory. J Chem Theory Comput 2015; 3:735-45. [PMID: 26627391 DOI: 10.1021/ct600367t] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The subsystem formulation of density functional theory is used to obtain equilibrium geometries and interaction energies for a representative set of noncovalently bound intermolecular complexes. The results are compared with literature benchmark data. The range of applicability of two considered approximations to the exchange-correlation- and nonadditive kinetic energy components of the total energy is determined. Local density approximation, which does not involve any empirical parameters, leads to excellent intermolecular equilibrium distances for hydrogen-bonded complexes (maximal error 0.13 Å for NH3-NH3). It is a method of choice for a wide class of weak intermolecular complexes including also dipole-bound and the ones formed by rare gas atoms or saturated hydrocarbons. The range of applicability of the chosen generalized gradient approximation, which was shown in our previous works to lead to good interaction energies in such complexes, where π-electrons are involved in the interaction, remains limited to this group because it improves neither binding energies nor equilibrium geometries in the wide class of complexes for which local density approximation is adequate. An efficient energy minimization procedure, in which optimization of the geometry and the electron density of each subsystem is made simultaneously, is proposed and tested.
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Affiliation(s)
- Marcin Dułak
- Département de Chimie Physique, Université de Genève, 30, quai Ernest-Ansermet, CH-1211 Genève 4, Switzerland, and Institute of Physical and Theoretical Chemistry, Wrocław University of Technology, Wyb. Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Jakub W Kamiński
- Département de Chimie Physique, Université de Genève, 30, quai Ernest-Ansermet, CH-1211 Genève 4, Switzerland, and Institute of Physical and Theoretical Chemistry, Wrocław University of Technology, Wyb. Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Tomasz A Wesołowski
- Département de Chimie Physique, Université de Genève, 30, quai Ernest-Ansermet, CH-1211 Genève 4, Switzerland, and Institute of Physical and Theoretical Chemistry, Wrocław University of Technology, Wyb. Wyspiańskiego 27, 50-370 Wrocław, Poland
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9
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Cerqueira NMFSA, Gonzalez PJ, Fernandes PA, Moura JJG, Ramos MJ. Periplasmic nitrate reductase and formate dehydrogenase: similar molecular architectures with very different enzymatic activities. Acc Chem Res 2015; 48:2875-84. [PMID: 26509703 DOI: 10.1021/acs.accounts.5b00333] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
It is remarkable how nature has been able to construct enzymes that, despite sharing many similarities, have simple but key differences that tune them for completely different functions in living cells. Periplasmic nitrate reductase (Nap) and formate dehydrogenase (Fdh) from the DMSOr family are representative examples of this. Both enzymes share almost identical three-dimensional protein foldings and active sites, in terms of coordination number, geometry and nature of the ligands. The substrates of both enzymes (nitrate and formate) are polyatomic anions that also share similar charge and stereochemistry. In terms of the catalytic mechanism, both enzymes have a common activation mechanism (the sulfur-shift mechanism) that ensures a constant coordination number around the metal ion during the catalytic cycle. In spite of these similarities, they catalyze very different reactions: Nap abstracts an oxygen atom from nitrate releasing nitrite, whereas FdH catalyzes a hydrogen atom transfer from formate and releases carbon dioxide. In this Account, a critical analysis of structure, function, and catalytic mechanism of the molybdenum enzymes periplasmic nitrate reductase (Nap) and formate dehydrogenase (Fdh) is presented. We conclude that the main structural driving force that dictates the type of reaction, catalyzed by each enzyme, is a key difference on one active site residue that is located in the top region of the active sites of both enzymes. In both enzymes, the active site is centered on the metal ion of the cofactor (Mo in Nap and Mo or W in Fdh) that is coordinated by four sulfur atoms from two pyranopterin guanosine dinucleotide (PGD) molecules and by a sulfido. However, while in Nap there is a Cys directly coordinated to the Mo ion, in FdH there is a SeCys instead. In Fdh there is also an important His that interacts very closely with the SeCys, whereas in Nap the same position is occupied by a Met. The role of Cys in Nap and SeCys in FdH is similar in both enzymes; however, Met and His have different roles. His participates directly on catalysis, and it is therefore detrimental for the catalytic cycle of FdH. Met only participates in substrate binding. We concluded that this small but key difference dictates the type of reaction that is catalyzed by each enzyme. In addition, it allows explaining why formate can bind in the Nap active site in the same way as the natural substrate (nitrate), but the reaction becomes stalled afterward.
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Affiliation(s)
- Nuno M. F. S. A. Cerqueira
- REQUIMTE/UCIBIO,
Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Pablo J. Gonzalez
- REQUIMTE/UCIBIO,
Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus de Caparica, 2829-516 Caparica, Portugal
| | - Pedro A. Fernandes
- REQUIMTE/UCIBIO,
Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - José J. G. Moura
- REQUIMTE/UCIBIO,
Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus de Caparica, 2829-516 Caparica, Portugal
| | - Maria João Ramos
- REQUIMTE/UCIBIO,
Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
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10
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Porcher JP, Fogeron T, Gomez-Mingot M, Derat E, Chamoreau LM, Li Y, Fontecave M. A Bioinspired Molybdenum Complex as a Catalyst for the Photo- and Electroreduction of Protons. Angew Chem Int Ed Engl 2015; 54:14090-3. [PMID: 26404460 DOI: 10.1002/anie.201505607] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Revised: 07/18/2015] [Indexed: 12/25/2022]
Abstract
A molybdenum-dithiolene-oxo complex was prepared as a model of some active sites of Mo/W-dependent enzymes. The ligand, a quinoxaline-pyran-fused dithiolene, mimics molybdopterin present in these active sites. For the first time, this type of complex was shown to be active as a catalyst for the photoreduction of protons with excellent turnover numbers (500) and good stability in aqueous/organic media and for the electroreduction of protons in acetonitrile with remarkable rate constants (1030 s(-1) at -1.3 V versus Ag/AgCl). DFT calculations provided insight into the catalytic cycle of the reaction, suggesting that the oxo ligand plays a key role in proton exchange. These results provide a basis to optimize this new class of H2 -evolving catalysts.
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Affiliation(s)
- Jean-Philippe Porcher
- Laboratoire de Chimie des Processus Biologiques, UMR 8229 CNRS, Collège de France, Université Paris 6, 11 Place Marcelin Berthelot, 75231 Paris Cedex 05 (France)
| | - Thibault Fogeron
- Laboratoire de Chimie des Processus Biologiques, UMR 8229 CNRS, Collège de France, Université Paris 6, 11 Place Marcelin Berthelot, 75231 Paris Cedex 05 (France)
| | - Maria Gomez-Mingot
- Laboratoire de Chimie des Processus Biologiques, UMR 8229 CNRS, Collège de France, Université Paris 6, 11 Place Marcelin Berthelot, 75231 Paris Cedex 05 (France)
| | - Etienne Derat
- Sorbonne Universités, UPMC Université Paris 6, Institut Parisien de Chimie Moléculaire, UMR 8232 CNRS, 4 place Jussieu, 75252 Paris Cedex 5 (France)
| | - Lise-Marie Chamoreau
- Sorbonne Universités, UPMC Université Paris 6, Institut Parisien de Chimie Moléculaire, UMR 8232 CNRS, 4 place Jussieu, 75252 Paris Cedex 5 (France)
| | - Yun Li
- Laboratoire de Chimie des Processus Biologiques, UMR 8229 CNRS, Collège de France, Université Paris 6, 11 Place Marcelin Berthelot, 75231 Paris Cedex 05 (France).
| | - Marc Fontecave
- Laboratoire de Chimie des Processus Biologiques, UMR 8229 CNRS, Collège de France, Université Paris 6, 11 Place Marcelin Berthelot, 75231 Paris Cedex 05 (France).
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11
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Porcher J, Fogeron T, Gomez‐Mingot M, Derat E, Chamoreau L, Li Y, Fontecave M. A Bioinspired Molybdenum Complex as a Catalyst for the Photo‐ and Electroreduction of Protons. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201505607] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Jean‐Philippe Porcher
- Laboratoire de Chimie des Processus Biologiques, UMR 8229 CNRS, Collège de France, Université Paris 6, 11 Place Marcelin Berthelot, 75231 Paris Cedex 05 (France)
| | - Thibault Fogeron
- Laboratoire de Chimie des Processus Biologiques, UMR 8229 CNRS, Collège de France, Université Paris 6, 11 Place Marcelin Berthelot, 75231 Paris Cedex 05 (France)
| | - Maria Gomez‐Mingot
- Laboratoire de Chimie des Processus Biologiques, UMR 8229 CNRS, Collège de France, Université Paris 6, 11 Place Marcelin Berthelot, 75231 Paris Cedex 05 (France)
| | - Etienne Derat
- Sorbonne Universités, UPMC Université Paris 6, Institut Parisien de Chimie Moléculaire, UMR 8232 CNRS, 4 place Jussieu, 75252 Paris Cedex 5 (France)
| | - Lise‐Marie Chamoreau
- Sorbonne Universités, UPMC Université Paris 6, Institut Parisien de Chimie Moléculaire, UMR 8232 CNRS, 4 place Jussieu, 75252 Paris Cedex 5 (France)
| | - Yun Li
- Laboratoire de Chimie des Processus Biologiques, UMR 8229 CNRS, Collège de France, Université Paris 6, 11 Place Marcelin Berthelot, 75231 Paris Cedex 05 (France)
| | - Marc Fontecave
- Laboratoire de Chimie des Processus Biologiques, UMR 8229 CNRS, Collège de France, Université Paris 6, 11 Place Marcelin Berthelot, 75231 Paris Cedex 05 (France)
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12
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Zhang HM, Chen SL. Include Dispersion in Quantum Chemical Modeling of Enzymatic Reactions: The Case of Isoaspartyl Dipeptidase. J Chem Theory Comput 2015; 11:2525-35. [DOI: 10.1021/acs.jctc.5b00246] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hai-Mei Zhang
- Key Laboratory
of Cluster
Science of Ministry of Education, Beijing Key Laboratory of Photoelectronic/Electrophotonic
Conversion Materials, School of Chemistry, Beijing Institute of Technology, Beijing 100081, China
| | - Shi-Lu Chen
- Key Laboratory
of Cluster
Science of Ministry of Education, Beijing Key Laboratory of Photoelectronic/Electrophotonic
Conversion Materials, School of Chemistry, Beijing Institute of Technology, Beijing 100081, China
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13
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Wesolowski TA, Shedge S, Zhou X. Frozen-Density Embedding Strategy for Multilevel Simulations of Electronic Structure. Chem Rev 2015; 115:5891-928. [DOI: 10.1021/cr500502v] [Citation(s) in RCA: 219] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Tomasz A. Wesolowski
- Department of Physical Chemistry, University of Geneva, CH-1211 Geneva 4, Switzerland
| | - Sapana Shedge
- Department of Physical Chemistry, University of Geneva, CH-1211 Geneva 4, Switzerland
| | - Xiuwen Zhou
- Department of Physical Chemistry, University of Geneva, CH-1211 Geneva 4, Switzerland
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14
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Cerqueira NMFSA, Pakhira B, Sarkar S. Theoretical studies on mechanisms of some Mo enzymes. J Biol Inorg Chem 2015; 20:323-35. [DOI: 10.1007/s00775-015-1237-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2014] [Accepted: 01/05/2015] [Indexed: 11/30/2022]
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15
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DFT study on the oxygen transfer mechanism in nitroethenediamine based H2-receptor antagonists using the bis-dithiolene complex as the model catalyst for N-oxide reductase enzyme. J Inorg Biochem 2014; 142:84-91. [PMID: 25450022 DOI: 10.1016/j.jinorgbio.2014.09.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Revised: 09/17/2014] [Accepted: 09/18/2014] [Indexed: 12/24/2022]
Abstract
Nitroethenediamine is an important functional unit, which is present in H2-receptor antagonists. These drugs show low bioavailability due to the bacterial degradation caused by the N-oxide reductase type of enzymes present in the human colon. Quantum chemical studies have been carried out to elucidate the mechanism of metabolic degradation of nitroethenediamine in the active site of N-oxide reductase. Three different pathways have been explored for the N-oxide bond cleavage by the model system, Mo(IV) bis-dithiolene complex [Mo(OMe)(mdt)2](-), (where mdt=1,2-dimethyl-ethene-1,2-dithiolate) using B3LYP/6-311+G(d,p) and M06/6-311+G(d,p) Density Functional Theory methods. The oxygen atom transfer from the nitrogen atom of nitroethenediamine to the Mo(IV) complex, involves simultaneous weakening of the N-oxide bond and the formation of Mo-O bond through a least motion path. During this transfer, Mo center is converted from a square pyramidal geometry to a distorted octahedral geometry, to facilitate the process of oxygen atom transfer. The energy barrier for the oxygen atom transfer from the imine tautomer has been estimated to be 25.9kcal/mol however, the overall reaction has been found to be endothermic. On the other hand, oxygen transfer reaction from the nitronic acid tautomer requires 30.5kcal/mol energy leading to a highly exothermic metabolite (M-1) directly hence, this path can be considered thermodynamically favorable for this metabolite. The alternative path involving the oxygen atom transfer from the enamine tautomer requires comparatively a higher energy barrier (32.6kcal/mol) and leads to a slightly endothermic metabolite. This study established the structural and energetic details associated with the Mo(IV) bis-dithiolene complex that catalyzes the degradation of nitroethenediamine based drug molecules.
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16
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Jacob CR, Neugebauer J. Subsystem density-functional theory. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2014. [DOI: 10.1002/wcms.1175] [Citation(s) in RCA: 229] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Christoph R. Jacob
- Center for Functional Nanostructures and Institute of Physical Chemistry; Karlsruhe Institute of Technology (KIT); Karlsruhe Germany
| | - Johannes Neugebauer
- Theoretische Organische Chemie, Organisch-Chemisches Institut; Westfälische Wilhelms-Universität Münster; Münster Germany
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17
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Blomberg MRA, Borowski T, Himo F, Liao RZ, Siegbahn PEM. Quantum chemical studies of mechanisms for metalloenzymes. Chem Rev 2014; 114:3601-58. [PMID: 24410477 DOI: 10.1021/cr400388t] [Citation(s) in RCA: 436] [Impact Index Per Article: 43.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Margareta R A Blomberg
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University , SE-106 91 Stockholm, Sweden
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18
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McGinnis WR, Audhya T, Edelson SM. Proposed toxic and hypoxic impairment of a brainstem locus in autism. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2013; 10:6955-7000. [PMID: 24336025 PMCID: PMC3881151 DOI: 10.3390/ijerph10126955] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Revised: 11/07/2013] [Accepted: 11/11/2013] [Indexed: 01/15/2023]
Abstract
Electrophysiological findings implicate site-specific impairment of the nucleus tractus solitarius (NTS) in autism. This invites hypothetical consideration of a large role for this small brainstem structure as the basis for seemingly disjointed behavioral and somatic features of autism. The NTS is the brain's point of entry for visceral afference, its relay for vagal reflexes, and its integration center for autonomic control of circulatory, immunological, gastrointestinal, and laryngeal function. The NTS facilitates normal cerebrovascular perfusion, and is the seminal point for an ascending noradrenergic system that modulates many complex behaviors. Microvascular configuration predisposes the NTS to focal hypoxia. A subregion--the "pNTS"--permits exposure to all blood-borne neurotoxins, including those that do not readily transit the blood-brain barrier. Impairment of acetylcholinesterase (mercury and cadmium cations, nitrates/nitrites, organophosphates, monosodium glutamate), competition for hemoglobin (carbon monoxide, nitrates/nitrites), and higher blood viscosity (net systemic oxidative stress) are suggested to potentiate microcirculatory insufficiency of the NTS, and thus autism.
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Affiliation(s)
- Woody R. McGinnis
- Autism Research Institute, 4182 Adams Avenue, San Diego, CA 92116, USA; E-Mail:
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +1-541-326-8822; Fax: +1-619-563-6840
| | - Tapan Audhya
- Division of Endocrinology, Department of Medicine, New York University Medical School, New York, NY 10016, USA; E-Mail:
| | - Stephen M. Edelson
- Autism Research Institute, 4182 Adams Avenue, San Diego, CA 92116, USA; E-Mail:
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Cerqueira NMFSA, Fernandes PA, Gonzalez PJ, Moura JJG, Ramos MJ. The sulfur shift: an activation mechanism for periplasmic nitrate reductase and formate dehydrogenase. Inorg Chem 2013; 52:10766-72. [PMID: 24066983 DOI: 10.1021/ic3028034] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
A structural rearrangement known as sulfur shift occurs in some Mo-containing enzymes of the DMSO reductase family. This mechanism is characterized by the displacement of a coordinating cysteine thiol (or SeCys in Fdh) from the first to the second shell of the Mo-coordination sphere metal. The hexa-coordinated Mo ion found in the as-isolated state cannot bind directly any exogenous ligand (substrate or inhibitors), while the penta-coordinated ion, attained upon sulfur shift, has a free binding site for direct coordination of the substrate. This rearrangement provides an efficient mechanism to keep a constant coordination number throughout an entire catalytic pathway. This mechanism is very similar to the carboxylate shift observed in Zn-dependent enzymes, and it has been recently detected by experimental means. In the present paper, we calculated the geometries and energies involved in the sulfur-shift mechanism using QM-methods (M06/(6-311++G(3df,2pd),SDD)//B3LYP/(6-31G(d),SDD)). The results indicated that the sulfur-shift mechanism provides an efficient way to enable the metal ion for substrate coordination.
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Affiliation(s)
- Nuno M F S A Cerqueira
- REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto , Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
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Why is the molybdenum-substituted tungsten-dependent formaldehyde ferredoxin oxidoreductase not active? A quantum chemical study. J Biol Inorg Chem 2013; 18:175-181. [PMID: 23183892 DOI: 10.1007/s00775-012-0961-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2012] [Accepted: 11/13/2012] [Indexed: 01/12/2023]
Abstract
Formaldehyde ferredoxin oxidoreductase is a tungsten-dependent enzyme that catalyzes the oxidative degradation of formaldehyde to formic acid. The molybdenum ion can be incorporated into the active site to displace the tungsten ion, but is without activity. Density functional calculations have been employed to understand the incapacitation of the enzyme caused by molybdenum substitution. The calculations show that the enzyme with molybdenum (Mo-FOR) has higher redox potential than that with tungsten, which makes the formation of the Mo(VI)=O complex endothermic by 14 kcal/mol. Following our previously suggested mechanism for this enzyme, the formaldehyde substrate oxidation was also investigated for Mo-FOR using the same quantum-mechanics-only model, except for the displacement of tungsten by molybdenum. The calculations demonstrate that formaldehyde oxidation occurs via a sequential two-step mechanism. Similarly to the tungsten-catalyzed reaction, the Mo(VI)=O species performs the nucleophilic attack on the formaldehyde carbon, followed by proton transfer in concert with two-electron reduction of the metal center. The first step is rate-limiting, with a total barrier of 28.2 kcal/mol. The higher barrier is mainly due to the large energy penalty for the formation of the Mo(VI)=O species.
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The prokaryotic Mo/W-bisPGD enzymes family: a catalytic workhorse in bioenergetic. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2013; 1827:1048-85. [PMID: 23376630 DOI: 10.1016/j.bbabio.2013.01.011] [Citation(s) in RCA: 103] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2012] [Revised: 01/21/2013] [Accepted: 01/23/2013] [Indexed: 01/05/2023]
Abstract
Over the past two decades, prominent importance of molybdenum-containing enzymes in prokaryotes has been put forward by studies originating from different fields. Proteomic or bioinformatic studies underpinned that the list of molybdenum-containing enzymes is far from being complete with to date, more than fifty different enzymes involved in the biogeochemical nitrogen, carbon and sulfur cycles. In particular, the vast majority of prokaryotic molybdenum-containing enzymes belong to the so-called dimethylsulfoxide reductase family. Despite its extraordinary diversity, this family is characterized by the presence of a Mo/W-bis(pyranopterin guanosine dinucleotide) cofactor at the active site. This review highlights what has been learned about the properties of the catalytic site, the modular variation of the structural organization of these enzymes, and their interplay with the isoprenoid quinones. In the last part, this review provides an integrated view of how these enzymes contribute to the bioenergetics of prokaryotes. This article is part of a Special Issue entitled: Metals in Bioenergetics and Biomimetics Systems.
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Gonzalez PJ, Rivas MG, Mota CS, Brondino CD, Moura I, Moura JJ. Periplasmic nitrate reductases and formate dehydrogenases: Biological control of the chemical properties of Mo and W for fine tuning of reactivity, substrate specificity and metabolic role. Coord Chem Rev 2013. [DOI: 10.1016/j.ccr.2012.05.020] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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23
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Mitra J, Sarkar S. Modelling the reduced xanthine oxidase in active sulfo and inactive desulfo forms. Dalton Trans 2013; 42:3050-8. [DOI: 10.1039/c2dt32309e] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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24
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Marino T, Russo N, Toscano M. Catalytic Mechanism of the Arylsulfatase Promiscuous Enzyme fromPseudomonas Aeruginosa. Chemistry 2012; 19:2185-92. [DOI: 10.1002/chem.201201943] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2012] [Revised: 11/06/2012] [Indexed: 11/11/2022]
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25
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Oxygenolysis reaction mechanism of copper-dependent quercetin 2,3-dioxygenase: A density functional theory study. Sci China Chem 2012. [DOI: 10.1007/s11426-012-4729-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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26
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Biaso F, Burlat B, Guigliarelli B. DFT Investigation of the Molybdenum Cofactor in Periplasmic Nitrate Reductases: Structure of the Mo(V) EPR-Active Species. Inorg Chem 2012; 51:3409-19. [DOI: 10.1021/ic201533p] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Frédéric Biaso
- Unité de Bioénergétique
et Ingénierie des Protéines, UMR 7281, Centre National
de la Recherche Scientifique, Institut de Microbiologie de la Méditerranée,
and Aix-Marseille University, 31 Chemin
Joseph Aiguier, 13402 Marseille Cedex 20, France
| | - Bénédicte Burlat
- Unité de Bioénergétique
et Ingénierie des Protéines, UMR 7281, Centre National
de la Recherche Scientifique, Institut de Microbiologie de la Méditerranée,
and Aix-Marseille University, 31 Chemin
Joseph Aiguier, 13402 Marseille Cedex 20, France
| | - Bruno Guigliarelli
- Unité de Bioénergétique
et Ingénierie des Protéines, UMR 7281, Centre National
de la Recherche Scientifique, Institut de Microbiologie de la Méditerranée,
and Aix-Marseille University, 31 Chemin
Joseph Aiguier, 13402 Marseille Cedex 20, France
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Silaghi-Dumitrescu R, Mich M, Matyas C, Cooper CE. Nitrite and nitrate reduction by molybdenum centers of the nitrate reductase type: Computational predictions on the catalytic mechanism. Nitric Oxide 2012; 26:27-31. [DOI: 10.1016/j.niox.2011.11.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2010] [Revised: 10/11/2011] [Accepted: 11/17/2011] [Indexed: 11/28/2022]
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Amata O, Marino T, Russo N, Toscano M. A Proposal for Mitochondrial Processing Peptidase Catalytic Mechanism. J Am Chem Soc 2011; 133:17824-31. [DOI: 10.1021/ja207065v] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Orazio Amata
- Dipartimento di Chimica and Centro di Calcolo ad Alte Prestazioni per Elaborazioni Parallele e Distribuite-Centro d'Eccellenza MURST, Universita' della Calabria, I-87030 Arcavacata di Rende (CS), Italy
| | - Tiziana Marino
- Dipartimento di Chimica and Centro di Calcolo ad Alte Prestazioni per Elaborazioni Parallele e Distribuite-Centro d'Eccellenza MURST, Universita' della Calabria, I-87030 Arcavacata di Rende (CS), Italy
| | - Nino Russo
- Dipartimento di Chimica and Centro di Calcolo ad Alte Prestazioni per Elaborazioni Parallele e Distribuite-Centro d'Eccellenza MURST, Universita' della Calabria, I-87030 Arcavacata di Rende (CS), Italy
| | - Marirosa Toscano
- Dipartimento di Chimica and Centro di Calcolo ad Alte Prestazioni per Elaborazioni Parallele e Distribuite-Centro d'Eccellenza MURST, Universita' della Calabria, I-87030 Arcavacata di Rende (CS), Italy
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29
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Liao RZ, Yu JG, Himo F. Tungsten-dependent formaldehyde ferredoxin oxidoreductase: Reaction mechanism from quantum chemical calculations. J Inorg Biochem 2011; 105:927-36. [DOI: 10.1016/j.jinorgbio.2011.03.020] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2011] [Revised: 03/25/2011] [Accepted: 03/28/2011] [Indexed: 11/30/2022]
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30
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Majumdar A, Sarkar S. Bioinorganic chemistry of molybdenum and tungsten enzymes: A structural–functional modeling approach. Coord Chem Rev 2011. [DOI: 10.1016/j.ccr.2010.11.027] [Citation(s) in RCA: 122] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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31
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32
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Alberto ME, Leopoldini M, Russo N. Can Human Prolidase Enzyme Use Different Metals for Full Catalytic Activity? Inorg Chem 2011; 50:3394-403. [DOI: 10.1021/ic1022517] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Marta E. Alberto
- Dipartimento di Chimica and Centro di Calcolo ad Alte Prestazioni per Elaborazioni Parallele e Distribuite-Centro d'Eccellenza MIUR, Universita' della Calabria, I-87030 Arcavacata di Rende (CS), Italy
| | - Monica Leopoldini
- Dipartimento di Chimica and Centro di Calcolo ad Alte Prestazioni per Elaborazioni Parallele e Distribuite-Centro d'Eccellenza MIUR, Universita' della Calabria, I-87030 Arcavacata di Rende (CS), Italy
| | - Nino Russo
- Dipartimento di Chimica and Centro di Calcolo ad Alte Prestazioni per Elaborazioni Parallele e Distribuite-Centro d'Eccellenza MIUR, Universita' della Calabria, I-87030 Arcavacata di Rende (CS), Italy
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33
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Mechanism of tungsten-dependent acetylene hydratase from quantum chemical calculations. Proc Natl Acad Sci U S A 2010; 107:22523-7. [PMID: 21149684 DOI: 10.1073/pnas.1014060108] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Acetylene hydratase is a tungsten-dependent enzyme that catalyzes the nonredox hydration of acetylene to acetaldehyde. Density functional theory calculations are used to elucidate the reaction mechanism of this enzyme with a large model of the active site devised on the basis of the native X-ray crystal structure. Based on the calculations, we propose a new mechanism in which the acetylene substrate first displaces the W-coordinated water molecule, and then undergoes a nucleophilic attack by the water molecule assisted by an ionized Asp13 residue at the active site. This is followed by proton transfer from Asp13 to the newly formed vinyl anion intermediate. In the subsequent isomerization, Asp13 shuttles a proton from the hydroxyl group of the vinyl alcohol to the α-carbon. Asp13 is thus a key player in the mechanism, but also W is directly involved in the reaction by binding and activating acetylene and providing electrostatic stabilization to the transition states and intermediates. Several other mechanisms are also considered but the energetic barriers are found to be very high, ruling out these possibilities.
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34
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Leopoldini M, Malaj N, Toscano M, Sindona G, Russo N. On the inhibitor effects of bergamot juice flavonoids binding to the 3-hydroxy-3-methylglutaryl-CoA reductase (HMGR) enzyme. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2010; 58:10768-10773. [PMID: 20843083 DOI: 10.1021/jf102576j] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Density functional theory was applied to study the binding mode of new flavonoids as possible inhibitors of the 3-hydroxy-3-methylglutaryl-CoA reductase (HMGR), an enzyme that catalyzes the four-electron reduction of HMGCoA to mevalonate, the committed step in the biosynthesis of sterols. The investigated flavonoid conjugates brutieridin and melitidin were recently quantified in the bergamot fruit extracts and identified to be structural analogues of statins, lipids concentration lowering drugs that inhibit HMGR. Computations allowed us to perform a detailed analysis of the geometrical and electronic features affecting the binding of these compounds, as well as that of the excellent simvastatin drug, to the active site of the enzyme and to give better insight into the inhibition process.
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Affiliation(s)
- Monica Leopoldini
- Dipartimento di Chimica, Università della Calabria, I-87036 Rende, CS, Italy
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35
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Dourado DFAR, Fernandes PA, Ramos MJ. Glutathione Transferase Classes Alpha, Pi, and Mu: GSH Activation Mechanism. J Phys Chem B 2010; 114:12972-80. [DOI: 10.1021/jp1053875] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Daniel F. A. R. Dourado
- REQUIMTE/Departamento de Química, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 687, 4169-007 Porto, Portugal
| | - Pedro Alexandrino Fernandes
- REQUIMTE/Departamento de Química, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 687, 4169-007 Porto, Portugal
| | - Maria João Ramos
- REQUIMTE/Departamento de Química, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 687, 4169-007 Porto, Portugal
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36
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Leopoldini M, Russo N, Toscano M. Favored Reaction Mechanism of Calcium-Dependent Phospholipase A2. Insights from Density Functional Exploration. J Phys Chem B 2010; 114:11584-93. [DOI: 10.1021/jp1003819] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Monica Leopoldini
- Dipartimento di Chimica and Centro di Calcolo ad Alte Prestazioni per Elaborazioni Parallele e Distribuite-Centro d’Eccellenza MIUR, Università della Calabria, I-87030 Arcavacata di Rende (CS), Italy
| | - Nino Russo
- Dipartimento di Chimica and Centro di Calcolo ad Alte Prestazioni per Elaborazioni Parallele e Distribuite-Centro d’Eccellenza MIUR, Università della Calabria, I-87030 Arcavacata di Rende (CS), Italy
| | - Marirosa Toscano
- Dipartimento di Chimica and Centro di Calcolo ad Alte Prestazioni per Elaborazioni Parallele e Distribuite-Centro d’Eccellenza MIUR, Università della Calabria, I-87030 Arcavacata di Rende (CS), Italy
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37
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Szaleniec M, Borowski T, Schühle K, Witko M, Heider J. Ab Inito Modeling of Ethylbenzene Dehydrogenase Reaction Mechanism. J Am Chem Soc 2010; 132:6014-24. [DOI: 10.1021/ja907208k] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Maciej Szaleniec
- Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30-239 Krakow, Poland, and Laboratory of Microbial Biochemistry, Philipps-University of Marburg, Marburg, Germany
| | - Tomasz Borowski
- Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30-239 Krakow, Poland, and Laboratory of Microbial Biochemistry, Philipps-University of Marburg, Marburg, Germany
| | - Karola Schühle
- Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30-239 Krakow, Poland, and Laboratory of Microbial Biochemistry, Philipps-University of Marburg, Marburg, Germany
| | - Malgorzata Witko
- Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30-239 Krakow, Poland, and Laboratory of Microbial Biochemistry, Philipps-University of Marburg, Marburg, Germany
| | - Johann Heider
- Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30-239 Krakow, Poland, and Laboratory of Microbial Biochemistry, Philipps-University of Marburg, Marburg, Germany
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38
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Amata O, Marino T, Russo N, Toscano M. Human insulin-degrading enzyme working mechanism. J Am Chem Soc 2010; 131:14804-11. [PMID: 19785409 DOI: 10.1021/ja9037142] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The possible mechanism by which the insulin-degrading enzyme (IDE) zinc-binding protease carries out its catalytic function toward two peptides of different length, simulating a portion of B chain of insulin, was investigated on an enzymatic model consisting of 130 /159 atoms, using the density functional theory method and the hybrid exchange-correlation functional B3LYP in gas phase and in the protein environment. Based on the geometry and relative stabilities of minima and transition states on the potential energy profiles, we determined that proteolysis reaction is exothermic and proceeds quickly as the barrier in the rate-limiting step falls widely within the range of values expected for an enzymatic catalysis, both in vacuum and in protein medium.
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Affiliation(s)
- Orazio Amata
- Dipartimento di Chimica and Centro di Calcolo ad Alte Prestazioni per Elaborazioni Parallele e Distribuite-Centro d'Eccellenza MURST, Universita' della Calabria, I-87030 Arcavacata di Rende (CS), Italy
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39
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Xie H, Cao Z. Enzymatic Reduction of Nitrate to Nitrite: Insight from Density Functional Calculations. Organometallics 2009. [DOI: 10.1021/om9008197] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Hujun Xie
- Department of Applied Chemistry, School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou 310035, People's Republic of China
| | - Zexing Cao
- Department of Chemistry and State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, People's Republic of China
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40
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The effect of the sixth sulfur ligand in the catalytic mechanism of periplasmic nitrate reductase. J Comput Chem 2009; 30:2466-84. [DOI: 10.1002/jcc.21280] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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41
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Leopoldini M, Russo N, Toscano M. Determination of the Catalytic Pathway of a Manganese Arginase Enzyme Through Density Functional Investigation. Chemistry 2009; 15:8026-8036. [DOI: 10.1002/chem.200802252] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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42
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Hofmann M. Density functional theory study of model complexes for the revised nitrate reductase active site in Desulfovibrio desulfuricans NapA. J Biol Inorg Chem 2009; 14:1023-35. [DOI: 10.1007/s00775-009-0545-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2008] [Accepted: 04/20/2009] [Indexed: 11/30/2022]
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43
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Orbital-Free Embedding Effective Potential in Analytically Solvable Cases. ADVANCES IN THE THEORY OF ATOMIC AND MOLECULAR SYSTEMS 2009. [DOI: 10.1007/978-90-481-2596-8_15] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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44
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The Oniom Method and its Applications to Enzymatic Reactions. CHALLENGES AND ADVANCES IN COMPUTATIONAL CHEMISTRY AND PHYSICS 2009. [DOI: 10.1007/978-1-4020-9956-4_2] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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45
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Pal K, Sarkar S. The Role of Axial Ligation in Nitrate Reductase: A Model Study by DFT Calculations on the Mechanism of Nitrate Reduction. Eur J Inorg Chem 2008. [DOI: 10.1002/ejic.200800514] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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46
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Leopoldini M, Chiodo S, Toscano M, Russo N. Reaction Mechanism of Molybdoenzyme Formate Dehydrogenase. Chemistry 2008; 14:8674-81. [DOI: 10.1002/chem.200800906] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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47
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Hofmann M. Electronic State of the Dimethyl Sulfoxide Reductase Active Site. Inorg Chem 2008; 47:5546-8. [DOI: 10.1021/ic800519d] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Matthias Hofmann
- Anorganisch-Chemisches Institut, Ruprecht-Karls-Universität Heidelberg, Im Neuenheimer Feld 270, 69120 Heidelberg, Germany
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48
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Experimental and theoretical study of a truly functional biomimetic molybdenum oxotransferase analogue system. J Inorg Biochem 2008; 102:1199-211. [DOI: 10.1016/j.jinorgbio.2008.01.029] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2007] [Revised: 01/17/2008] [Accepted: 01/18/2008] [Indexed: 11/19/2022]
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49
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Leopoldini M, Marino T, Toscano M. Theoretical investigation of the catalytic mechanism of the protein arginine deiminase 4 enzyme. Theor Chem Acc 2008. [DOI: 10.1007/s00214-008-0433-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Chen SL, Fang WH, Himo F. Technical aspects of quantum chemical modeling of enzymatic reactions: the case of phosphotriesterase. Theor Chem Acc 2008. [DOI: 10.1007/s00214-008-0430-y] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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